file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
length(assayed_genes)## [1] 2000
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 32.00 36.75 38.00 37.58 39.00 42.00
## [1] 40
## [1] 32 33 34 34 35 35 36 36 36 36 37 37 37 37 37 37 37 37 37 38 38 38 38 38 38
## [26] 38 38 38 39 39 39 40 40 40 40 40 40 41 41 42
alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}
table(is.na(a2s))##
## FALSE TRUE
## 1739 261
##
## FALSE TRUE <NA>
## 21 1718 261
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: LRRC6 DNAAF11
## 2: C11orf49 CSTPP1
## 3: LINC00476 ERCC6L2-AS1
## 4: HNRNPA1P48 HNRNPA1L3
## 5: ZRANB2-AS2 ZRANB2-DT
## 6: LINC00271 AHI1-DT
## 7: RFX3-AS1 RFX3-DT
## 8: LINC00884 ATP13A3-DT
## 9: FBXO30-DT EPM2A-DT
## 10: LINC00894 EOLA2-DT
## 11: COX10-AS1 COX10-DT
## 12: LINC01184 SLC12A2-DT
## 13: FAM198B-AS1 GASK1B-AS1
## 14: C5orf17 LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16: LINC01146 HISLA
## 17: BTBD11 ABTB3
## 18: H2BU1 H2BC26
## 19: SKIV2L SKIC2
## 20: FAM155A NALF1
## 21: CTB-41I6.2 PIK3R5-DT
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CFTR CFTR CFTR
## 2: ICA1 ICA1 ICA1
## 3: PDK4 PDK4 PDK4
## 4: CALCR CALCR CALCR
## 5: ABCB4 ABCB4 ABCB4
## t1
## 1
## 2000
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
## [1] 1587110 4
## Gene Gene name Cell type nTPM
## 1: ENSG00000000003 TSPAN6 Adipocytes 149.5
## 2: ENSG00000000003 TSPAN6 Alveolar cells type 1 6.1
## 3: ENSG00000000003 TSPAN6 Alveolar cells type 2 10.5
## 4: ENSG00000000003 TSPAN6 Astrocytes 13.9
## 5: ENSG00000000003 TSPAN6 B-cells 1.5
## [1] 79
##
## Adipocytes Alveolar cells type 1
## 20090 20090
## Alveolar cells type 2 Astrocytes
## 20090 20090
## B-cells Basal keratinocytes
## 20090 20090
## Basal prostatic cells Basal respiratory cells
## 20090 20090
## Basal squamous epithelial cells Bipolar cells
## 20090 20090
## Breast glandular cells Breast myoepithelial cells
## 20090 20090
## Cardiomyocytes Cholangiocytes
## 20090 20090
## Club cells Collecting duct cells
## 20090 20090
## Cone photoreceptor cells Cytotrophoblasts
## 20090 20090
## dendritic cells Distal enterocytes
## 20090 20090
## Distal tubular cells Ductal cells
## 20090 20090
## Early spermatids Endometrial ciliated cells
## 20090 20090
## Endometrial stromal cells Endothelial cells
## 20090 20090
## Enteroendocrine cells Erythroid cells
## 20090 20090
## Excitatory neurons Exocrine glandular cells
## 20090 20090
## Extravillous trophoblasts Fibroblasts
## 20090 20090
## Gastric mucus-secreting cells Glandular and luminal cells
## 20090 20090
## granulocytes Granulosa cells
## 20090 20090
## Hepatocytes Hofbauer cells
## 20090 20090
## Horizontal cells Inhibitory neurons
## 20090 20090
## Intestinal goblet cells Ionocytes
## 20090 20090
## Kupffer cells Langerhans cells
## 20090 20090
## Late spermatids Leydig cells
## 20090 20090
## Macrophages Melanocytes
## 20090 20090
## Microglial cells monocytes
## 20090 20090
## Mucus glandular cells Muller glia cells
## 20090 20090
## NK-cells Oligodendrocyte precursor cells
## 20090 20090
## Oligodendrocytes Pancreatic endocrine cells
## 20090 20090
## Paneth cells Peritubular cells
## 20090 20090
## Plasma cells Prostatic glandular cells
## 20090 20090
## Proximal enterocytes Proximal tubular cells
## 20090 20090
## Respiratory ciliated cells Rod photoreceptor cells
## 20090 20090
## Salivary duct cells Schwann cells
## 20090 20090
## Serous glandular cells Sertoli cells
## 20090 20090
## Skeletal myocytes Smooth muscle cells
## 20090 20090
## Spermatocytes Spermatogonia
## 20090 20090
## Squamous epithelial cells Suprabasal keratinocytes
## 20090 20090
## Syncytiotrophoblasts T-cells
## 20090 20090
## Theca cells Thymic epithelial cells
## 20090 20090
## Undifferentiated cells
## 20090
## [1] 16 2
## Cell_type Cell_group
## 1: Excitatory neurons Neuronal
## 2: Inhibitory neurons Neuronal
##
## Astrocytes B-cells
## 20090 20090
## Bipolar cells Cone photoreceptor cells
## 20090 20090
## Excitatory neurons Horizontal cells
## 20090 20090
## Inhibitory neurons Microglial cells
## 20090 20090
## Muller glia cells Oligodendrocyte precursor cells
## 20090 20090
## Oligodendrocytes Plasma cells
## 20090 20090
## Rod photoreceptor cells Schwann cells
## 20090 20090
## T-cells
## 20090
## [1] 2000 3
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info[sym_in_data %in% gene_sets[[k]], gene_symbol]
n_genes = sum(genes %in% ct$`Gene name`)
print(sprintf("found %d genes.", n_genes))
if(n_genes == 0) { next }
df = ct[`Gene name` %in% genes,]
dim(df)
df[1:2,]
stopifnot(all(str_to_lower(df$`Cell type`) %in%
str_to_lower(cell_group$Cell_type)))
mat1 = match(str_to_lower(df$`Cell type`),
str_to_lower(cell_group$Cell_type))
df = cbind(df, cell_group[mat1,])
df[1:2,]
df$Cell_type = factor(df$Cell_type, levels = cell_group$Cell_type)
df$Cell_group = factor(df$Cell_group,
levels = unique(cell_group$Cell_group))
p1 = ggplot(df, aes(x=Cell_type, y=log10(nTPM + 0.1), fill=Cell_group)) +
geom_boxplot() + xlab("Cell type") + ggtitle(set_k) +
theme(axis.text.x = element_text(angle = 45, hjust = 1)) +
scale_fill_brewer(palette="RdBu")
print(p1)
}## [1] 1
## [1] "SYT7" "CDH20" "NALCN" "ARFGEF3"
## [5] "ADAM23" "DNAH6" "CHD5" "CSMD2"
## [9] "PCSK2" "ATP8A2" "CBLN2" "STXBP5L"
## [13] "TENM2" "CNTN5" "ZNF385D" "AK5"
## [17] "CLSTN2" "ANKRD30BL" "RANBP3L" "ADGRV1"
## [21] "AMER2" "GREM1" "FSTL5" "FUT9"
## [25] "HPSE2" "SRRM3" "SSTR2" "FLRT2"
## [29] "CACNA1E" "LINC00632" "BASP1-AS1" "ROR1-AS1"
## [33] "RP11-191L9.4" "AC093843.1" "LINC01435" "RP11-384F7.2"
## [37] "CTC-340A15.2" "SLC5A4-AS1" "CTC-535M15.2" "RMST"
## [41] "RP11-436D23.1"
## [1] "found 29 genes."
## [1] 2
## [1] "PDK4" "ABCB4" "CPED1" "GASK1A"
## [5] "SESN3" "TENM4" "GASK1B" "FOLR2"
## [9] "ARHGAP42" "PLD4" "CYSLTR1" "C5orf64"
## [13] "RAB39A" "CLEC9A" "MAMDC2-AS1" "AC003090.1"
## [17] "LMCD1-AS1" "HDAC2-AS2" "LINC02642" "RP11-634B7.4"
## [21] "COX10-AS1" "AC008697.1" "LINC01301" "LINC01094"
## [25] "MAILR" "MIR3142HG" "RP11-946L16.1" "RP11-554D14.6"
## [29] "RP11-187O7.3" "MRC1" "MIR222HG" "MIR223HG"
## [33] "LINC00506" "RP11-323F24.5" "RP11-685G11.1" "RP11-4F5.3"
## [37] "CPM" "KCNE1"
## [1] "found 16 genes."
## [1] 3
## [1] "SIGLEC1" "ADGRD1" "F13A1" "LILRB2"
## [5] "ENOSF1" "IFI44L" "CH25H" "FHAD1"
## [9] "TMEM163" "ADAMTS15" "PGBD5" "ODF3B"
## [13] "PLCXD3" "MS4A4E" "RP11-445F6.2" "LINC01515"
## [17] "AC092431.3" "LINC02008" "BDNF-AS" "LINC02211"
## [21] "LINC02432" "C5orf17" "LINC02196" "FAM66D"
## [25] "OVCH1-AS1" "RP11-72M17.1" "CTD-2336H13.2" "LINC02073"
## [29] "RP11-154H12.3" "RP11-354K4.2" "CCDC28A-AS1" "LINC01374"
## [33] "RP11-281A20.2" "CERNA2" "RP11-221G19.1" "RP11-321P16.3"
## [37] "RP13-52K8.2"
## [1] "found 14 genes."
## [1] 4
## [1] "ACER3" "CARMIL1" "SYNDIG1" "FAM149A"
## [5] "TBC1D14" "NPL" "NKD1" "AOPEP"
## [9] "DISP1" "SAMSN1" "DEPTOR" "DENND2B"
## [13] "ATF7IP2" "TMC7" "SPTLC3" "SCAI"
## [17] "ZDHHC14" "KCNQ3" "PRKN" "RANBP17"
## [21] "LINC02649" "MIR99AHG" "RP1-30E17.2" "HMGA1P4"
## [25] "ZFPM2-AS1" "RP11-10H3.1" "RP11-692P14.1" "RP6-91H8.6"
## [29] "ARHGAP6" "KCNQ2" "RAP1GAP" "PILRA"
## [33] "GRK3" "PADI2" "SEC14L1" "SLC2A13"
## [37] "KCNQ5" "LNCAROD"
## [1] "found 29 genes."
## [1] 5
## [1] "MGLL" "PRTFDC1" "NIPAL2" "MAP2K6"
## [5] "IFT43" "CCDC18" "SSPN" "GSTCD"
## [9] "MED12L" "FILIP1L" "GPR34" "CENPP"
## [13] "RP5-1132H15.1" "RMDN2-AS1" "RP11-692D12.1" "LINC00624"
## [17] "HGF" "TGFB2" "TMED8" "CLNK"
## [21] "HPCAL1" "TOX2" "TMEM115" "GYPC"
## [25] "FAM117B" "CCDC40" "IQGAP2" "HTR7"
## [29] "PARP8" "PCNT" "RHOBTB3" "ABCA1"
## [33] "GLRX" "GOLIM4" "EFCAB2" "SLC48A1"
## [37] "SBF2-AS1" "RP11-154H23.4"
## [1] "found 32 genes."
## [1] 6
## [1] "HHAT" "ZNF821" "MOBP" "AATK" "ST3GAL1"
## [6] "FAM50A" "RGS1" "MTMR8" "ADAP1" "MEGF9"
## [11] "SNX25" "DARS1" "CDH26" "SEM1" "AFDN"
## [16] "KIAA0513" "GPNMB" "CCNG2" "ARHGAP18" "TIAM2"
## [21] "RSU1" "FRRS1" "ABCG1" "ANKZF1" "MARCHF8"
## [26] "APLF" "MFSD4B" "ZC3H6" "DPYD" "PARVB"
## [31] "H1-0" "CYRIA" "GCC2-AS1" "AC093818.1" "PIK3IP1-DT"
## [36] "MIR181A1HG" "IFITM10" "CLEC5A"
## [1] "found 34 genes."
## [1] 7
## [1] "SLC4A7" "EPB41L2" "POLA1" "TGFBR1" "SIPA1L2" "BIN1"
## [7] "BACH1" "SOCS6" "SH3RF3" "FNDC3B" "TRIP11" "TJP1"
## [13] "ARHGEF10" "DDX5" "GAB1" "E2F3" "P4HA1" "RASSF8"
## [19] "RUNX2" "ARHGAP22" "UACA" "FNBP1L" "MSN" "MCPH1"
## [25] "MGAT5" "RUNX1" "ZNF143" "AXL" "LDLRAD4" "ALCAM"
## [31] "PEAK1" "SND1"
## [1] "found 32 genes."
## [1] 8
## [1] "PDE10A" "GNLY" "ADAMTS19" "GLT1D1"
## [5] "BANK1" "ADAMTS3" "UCN" "MT1E"
## [9] "TMEM151B" "RFLNA" "ZNF804B" "LINC01277"
## [13] "AC073115.7" "AC002539.1" "RP3-525N10.2" "LINC00271"
## [17] "KIF5C-AS1" "LINC02884" "AC007682.1" "AC073115.6"
## [21] "MIR4300HG" "STARD4-AS1" "LINC00923" "LINC02055"
## [25] "RP4-809F18.1" "MTRNR2L8" "LINC02316" "PSMD7-DT"
## [29] "RP11-621L6.2" "RP11-58G13.1" "RP11-413N10.3" "RP11-640F22.1"
## [33] "LINC02885" "RP11-38B6.1" "RP11-320L2.1" "RP11-341N18.1"
## [1] "found 12 genes."
## [1] 9
## [1] "HTR2B" "PNMA3" "ZNRF1" "NFIX" "NSMAF" "PDE8A"
## [7] "GRAMD4" "FOSL2" "TBC1D2" "PCSK5" "RNF24" "BNIP3L"
## [13] "GYS1" "PPARD" "PFKFB4" "GBE1" "PAPOLG" "NR4A3"
## [19] "ATF1" "KDM6B" "PHF21A" "GLUL" "GABARAPL1" "PELI2"
## [25] "GNA12" "SLC25A37" "ARID5B" "CFDP1" "MAPK13" "SPRY1"
## [31] "NFIL3" "PPIP5K1" "KLHL6" "PPP1R3B" "BNIP3" "TRNAU1AP"
## [37] "LIMK2"
## [1] "found 37 genes."
## [1] 10
## [1] "SCMH1" "KIFAP3"
## [3] "APBB1IP" "TMEM156"
## [5] "SPATA6" "FRMD6"
## [7] "KCNMB1" "RASGEF1C"
## [9] "KCNMA1" "AUTS2"
## [11] "TAGAP" "TMEM52B"
## [13] "NAV2" "ZNF608"
## [15] "TLN2" "GAP43"
## [17] "OLR1" "DLEU1"
## [19] "B3GNT5" "NCKAP5"
## [21] "SPATA13_ENSG00000182957" "SLC8A1"
## [23] "SFMBT2" "MBD5"
## [25] "TMSB4X" "LTC4S"
## [27] "RP11-557H15.4" "LINC02232"
## [29] "RP11-419I17.1" "RNASET2"
## [31] "RGCC" "ZBTB46"
## [33] "PCGF5" "FMN1"
## [1] "found 29 genes."
## [1] 11
## [1] "MUSK" "EFR3B"
## [3] "PROCR" "CRYM"
## [5] "STMN2" "ECM2"
## [7] "OPRM1" "PODXL2"
## [9] "NEK11" "WLS"
## [11] "IFIT3" "IFIT2"
## [13] "FMO5" "ABCA8"
## [15] "MMS22L" "IER2"
## [17] "FAM227B" "BEAN1"
## [19] "GLYATL1" "MYO5B"
## [21] "SLC35G2" "CPLX1"
## [23] "DTWD2" "DENND5B"
## [25] "GRIK1" "PC"
## [27] "MCMDC2" "TSPYL2"
## [29] "IFIT1" "STMN3"
## [31] "H2BC18" "SMCR5"
## [33] "GPRC5D-AS1" "LINC01605_ENSG00000253161"
## [35] "RP11-867G2.8" "RP11-314L11.1"
## [37] "TMEM140"
## [1] "found 32 genes."
## [1] 12
## [1] "PLPP1" "HAMP" "AZIN2" "SHOC1"
## [5] "NLGN4Y" "MICOS10" "ADGRG2" "TTTY14"
## [9] "FLJ40194" "DLEU7" "COL25A1" "EDNRB-AS1"
## [13] "ENTPD1-AS1" "SLC8A1-AS1" "RP11-202G18.1" "HCG22"
## [17] "CCDC26" "RP11-142M10.2" "LINC00884" "RNASEH2B-AS1"
## [21] "RP11-353M9.1" "CCDC200" "RP11-360F5.1" "LINC02057"
## [25] "LINC01258" "RP11-238K6.1" "RP11-624C23.1" "RP11-452H21.1"
## [29] "SMIM35" "RP11-196H14.2" "RP11-136F16.1" "LINC00621"
## [33] "CEACAM16-AS1" "RP11-399K21.11" "LINC02712" "RP11-323P17.2"
## [37] "RP11-264E23.4" "RP11-13J12.3"
## [1] "found 11 genes."
## [1] 13
## [1] "ATP8B1" "SLC5A9" "SGCE" "PDE5A"
## [5] "ENO4" "FAM177B" "INSYN2B" "ANKUB1"
## [9] "AC002463.3" "ARHGAP26-AS1" "AC017101.10" "AC096558.1"
## [13] "SRGAP2-AS1" "AC083884.8" "AC037445.1" "RP11-666F17.1"
## [17] "CPB2-AS1" "MYCBP2-AS1" "DIAPH2-AS1" "AC018890.6"
## [21] "CTD-2015H6.3" "CTD-2227I18.1" "RHOQ-AS1" "RP11-649G15.2"
## [25] "AP000487.6" "RP11-513G19.1" "USP3-AS1" "RP11-815J21.4"
## [29] "RP11-16B9.1" "ABHD15-AS1" "RP11-16C1.3" "RP11-793A3.2"
## [33] "RP11-53B2.3" "CTD-2282P23.2" "RP11-793H13.14" "DISC2"
## [37] "RP11-65F13.4" "RP11-1146N6.3" "AC009505.4"
## [1] "found 8 genes."
## [1] 14
## [1] "ZFP64" "NEXMIF" "CASS4" "PITPNM2"
## [5] "PLCL1" "BEX1" "RALGPS1" "GPAT3"
## [9] "RAB40B" "NRGN" "TSPAN7" "PLXDC1"
## [13] "SMIM14" "NXN" "MIR31HG" "MACROD2"
## [17] "FIGN" "LIPE-AS1" "ALOX12-AS1" "KIF9-AS1"
## [21] "RP11-120D5.1" "RP11-246A10.1" "MRPS30-DT" "RP11-370I10.6"
## [25] "LINC01572" "RP11-495L19.1" "TENM1" "ADGRL1"
## [29] "GDF11" "PLXNC1" "CFAP161" "ST3GAL2"
## [33] "CXXC5" "CDH4" "ANKS1B" "CTD-3088G3.8"
## [37] "SYCP2" "RORB" "LL22NC03-2H8.5"
## [1] "found 27 genes."
## [1] 15
## [1] "ADAM28" "ST6GAL1" "IPCEF1" "PLAT" "IGSF21"
## [6] "RCAN3" "PLAU" "ITPR2" "ABCC4" "C3"
## [11] "FOXP2" "LYVE1" "GARNL3" "GIPC2" "GAREM1"
## [16] "AIG1" "FRMD4A" "PRMT9" "CX3CR1" "P2RY12"
## [21] "LRRC8C" "CA8" "SLC9A9" "CH17-55D9.1" "ARHGAP15"
## [26] "SLC1A3" "IL27RA" "LIFR" "FOXP1" "OGFRL1"
## [31] "SLC41A2" "CSGALNACT1" "JAZF1" "MTSS1" "BNC2"
## [36] "MAML2" "IFNLR1"
## [1] "found 36 genes."
## [1] 16
## [1] "HIVEP2" "SLC9A7" "HDHD5" "MAP3K20"
## [5] "ARRDC2" "AK1" "STN1" "MXI1"
## [9] "GTDC1" "ATP8A1" "CEMIP2" "RASGEF1B"
## [13] "PGGHG" "ST18" "SLC26A7" "ZFYVE28"
## [17] "KLF13" "RESF1" "LPCAT4" "RBM44"
## [21] "TMTC2" "TNFAIP8L3" "NCMAP" "ZNF395"
## [25] "TPRG1" "ERO1A" "LINC02397" "AS3MT"
## [29] "FAM229A" "SGO1-AS1" "DIRC3" "DARS1-AS1"
## [33] "LINC01762" "AF064858.8" "RP11-305L7.3" "FMNL1-DT"
## [37] "LINC01138" "MYOCOS" "RP11-344F5.1" "RP11-249L21.6"
## [1] "found 29 genes."
## [1] 17
## [1] "MMP24" "GLIPR1L1" "EYS" "FSIP2"
## [5] "SPDYE2" "HDAC4-AS1" "ELMO1-AS1" "TMLHE-AS1"
## [9] "HNRNPA1P48" "LINC01375" "AC105461.1" "RP11-165F24.3"
## [13] "RP11-526K17.2" "ALG13-AS1" "RP1-225E12.2" "COA6-AS1"
## [17] "RP11-528G1.2" "RP11-575L7.8" "BCL2L1-AS1" "DENND6A-AS1"
## [21] "ZBTB20-AS5" "LINC00960" "RP11-712B9.2" "MEF2C-AS2"
## [25] "RP11-268P4.5" "RP11-39E3.3" "RP11-506H20.1" "RP11-434H14.1"
## [29] "RP11-370I10.2" "CTD-2647E9.3" "RP11-317G6.1" "RP11-703M24.5"
## [33] "CTD-3149D2.4" "RP4-769N13.7" "RP1-256G22.2" "RP11-121C2.3"
## [37] "RP11-7F3.1" "RP11-685G9.5" "RP11-555K12.4" "RP11-56I23.2"
## [1] "found 5 genes."
## [1] 18
## [1] "ZFY" "SLC26A3"
## [3] "PCDH11Y" "PXDNL"
## [5] "NR6A1" "SEMA3E"
## [7] "FUT10" "LRRC3B"
## [9] "CCDC73" "POTEG"
## [11] "RP11-37N22.1" "AC023469.1"
## [13] "AC067959.1" "RP11-147G16.1"
## [15] "RP11-154D17.1" "MYO16-AS1"
## [17] "AC013463.2" "LINC02646"
## [19] "AC002066.1" "CTD-2643I7.5"
## [21] "RP11-696N14.1" "RP11-17A1.3"
## [23] "RP11-259O2.1" "RP11-79E3.2"
## [25] "LINC01609" "RP11-351A11.1"
## [27] "RP11-13N12.1" "RP11-20D14.3"
## [29] "MTRNR2L12" "RMRP_ENSG00000269900"
## [31] "SCARNA2_ENSG00000270066" "AGBL1"
## [33] "CH507-513H4.1" "CH507-528H12.1"
## [35] "RP11-596C23.6" "RP4-799O8.1"
## [37] "RP11-322M13.1" "AC003099.2"
## [39] "RP11-398J12.1" "RP11-404C6.6"
## [1] "found 12 genes."
## [1] 19
## [1] "RPL3" "RPL18A" "RPL19" "RPL34"
## [5] "RPL24" "FGF13" "MTHFS" "RPS24"
## [9] "PRDM5" "RPS2" "RPS11" "RPL11"
## [13] "SPAG16" "RPL32" "FAU" "ATG10"
## [17] "RPL26" "ELAVL4" "MRPL1" "RPL38"
## [21] "RPLP2" "RPS23" "SPATS2L" "CPNE4"
## [25] "RPL12" "RPL23A" "RPL39" "AIF1"
## [29] "RP11-535M15.1" "LINC01278" "PVT1" "RP11-37B2.1"
## [33] "SLC1A2" "LPL" "ADARB1" "LILRB3"
## [1] "found 32 genes."
## [1] 20
## [1] "STS" "MID1" "CCDC170" "DOCK10" "IRF8"
## [6] "ITGA9" "AC097721.2" "XIST" "TWIST2" "MEI4"
## [11] "SCIN" "LCP2" "CTTNBP2" "DOCK9" "IRAK3"
## [16] "INTS6" "NCOA7" "TSHZ3" "PTPRE" "PRAM1"
## [21] "CCNH" "FAM13A" "SSH2" "USP53" "SDK1"
## [26] "DIXDC1" "FER" "ACSL1" "MERTK" "GPHN"
## [31] "CHD2" "CMSS1" "GPRIN3" "MITF" "RALGAPA2"
## [36] "PLCG2"
## [1] "found 34 genes."
## [1] 21
## [1] "MPP2" "ATF5" "FGR" "LRRC7" "CDK14" "CDK17"
## [7] "ARHGAP10" "IGSF9B" "ITPKC" "HIVEP1" "FGF14" "POU6F2"
## [13] "CPE" "MOB3B" "RAMP1" "MACROD1" "PDZD2" "CNKSR2"
## [19] "ADGRL3" "LONRF1" "NCAM2" "SORCS3" "GMEB1" "CSMD3"
## [25] "CRADD" "NLGN1" "CTNND2" "PTGER4" "NEGR1" "CNTNAP2"
## [31] "CADM2" "ZBTB7A" "NRXN1" "ZBTB7C" "LSAMP" "NRG3"
## [37] "SNHG14"
## [1] "found 36 genes."
## [1] 22
## [1] "ICA1" "MCF2L2" "IL1A" "ZRANB3" "EFCAB11"
## [6] "TCERG1L" "KCNMB2" "CTA-292E10.6" "LINC00996" "KCNQ1OT1"
## [11] "AC009166.9" "CNTN1" "NCDN" "HPCAL4" "SLC2A5"
## [16] "CACNA1B" "CACNA1C" "SCN3A" "CACNA2D1" "PTPRN2"
## [21] "SYN2" "SPTBN4" "EDIL3" "RBFOX3" "GRM5"
## [26] "KCND3" "DPP10" "MSRA" "PCDH9" "KCND2"
## [31] "PRKG1" "SYN3" "GRM7" "FAM153CP" "U91319.1"
## [1] "found 29 genes."
## [1] 23
## [1] "CEACAM1" "SLC9B1" "RP11-281P23.2" "RP11-493L12.3"
## [5] "RP11-516C1.1" "CELSR3" "ABCA7" "PLEKHH3"
## [9] "ANO8" "MLF2" "GALNT16" "HELLS"
## [13] "TGFBI" "HIF3A" "CHI3L1" "FGF17"
## [17] "LYPD5" "TNFRSF11B" "ADCY5" "H2AC6"
## [21] "VMO1" "NHEJ1" "EME2" "ZNF521"
## [25] "ZDBF2" "AF064858.6" "SLC12A8" "RP11-384C4.7"
## [29] "RP3-467L1.4" "RP11-657O9.1" "ARHGEF25" "LINC01414"
## [33] "RP11-661A12.5" "MTRNR2L1" "RP11-429A20.3" "RP11-81K2.1"
## [37] "LINC00551"
## [1] "found 25 genes."
## [1] 24
## [1] "ZDHHC19" "RP11-713N11.4" "PKD1" "SLC2A3"
## [5] "DDX3Y" "HACE1" "PPP1R15A" "GADD45B"
## [9] "RNMT" "FLT1" "IL4I1" "APBB3"
## [13] "USP9Y" "SPP1" "SRGN" "TREM1"
## [17] "MICAL2" "RGS16" "MYO10" "PLIN2"
## [21] "TAMALIN" "ALDH1A1" "DDIT4" "FAM210A"
## [25] "ADSS1" "ANKRD37" "IARS1" "H2BU1"
## [29] "CEBPD" "ZSCAN31" "HIF1A-AS3" "CTD-2285E13.1"
## [33] "RP11-134L10.2"
## [1] "found 28 genes."
## [1] 25
## [1] "CALCR" "IL7" "NEURL2" "PIGC"
## [5] "ADGRA3" "ADGRG5" "RNF180" "LINC00476"
## [9] "IRAG1-AS1" "CATSPERE" "SDHAF3" "SCOC-AS1"
## [13] "PAPSS2" "CARNMT1-AS1" "ATP6AP1L" "ENTPD3-AS1"
## [17] "TMEM72-AS1" "TSBP1-AS1" "RP13-188A5.1" "RP5-1198O20.4"
## [21] "FSIP2-AS1" "IPO9-AS1" "UFL1-AS1" "RPL34-DT"
## [25] "RP11-195C7.1" "LRIG2-DT" "LINC01877" "RORA-AS1"
## [29] "STX18-AS1" "RP11-130F10.1" "LIX1-AS1" "DISC1FP1"
## [33] "RP11-160E2.6" "RP11-74J13.8" "EIF1B-AS1" "RP11-736I24.5"
## [37] "RP11-19D22.1" "RP11-622O11.6" "RP11-261A24.1" "RP11-237N2.1"
## [41] "RP1-236J16.3" "RP11-120L14.1"
## [1] "found 10 genes."
## [1] 26
## [1] "ERCC8" "DHRS9" "ANGPT2" "CHN1"
## [5] "UBE2Q2" "BCL2A1" "TNFRSF21" "IRAK1BP1"
## [9] "TEX9" "ABCA5" "PAQR3" "LCLAT1"
## [13] "RP11-131L23.1" "RPL41" "VCAN" "KCNAB2"
## [17] "MYOM1" "KATNAL1" "SPOCK2" "SLC16A10"
## [21] "GABRG2" "CYTIP" "HIP1" "BTG1"
## [25] "PITPNC1" "RASA2" "ZMAT4" "OTUD1"
## [29] "ATOH8" "C11orf80" "MCTP1" "JAKMIP2"
## [33] "CD247" "TOX" "MIR155HG" "LUCAT1"
## [37] "RP11-475M20.2"
## [1] "found 33 genes."
## [1] 27
## [1] "DERA" "TDRD3" "DAAM1" "GDAP1" "ARSB" "EPHB2"
## [7] "STAMBPL1" "NUBPL" "NFIA" "KIF26B" "ARHGAP25" "DYNC2H1"
## [13] "CCDC7" "CLEC16A" "LIMCH1" "RFX3" "PHLPP1" "RFX2"
## [19] "TRPS1" "PRKAG2" "SASH1" "ELL2" "IQSEC2" "IQSEC1"
## [25] "FARP1" "MSI2" "RBM47" "SLC43A2" "DHRSX" "AFF1"
## [31] "PACS1" "SAMD12" "SERTAD2" "GDI1"
## [1] "found 34 genes."
## [1] 28
## [1] "RIPOR2" "DUOX1" "MCTP2" "TMEM44"
## [5] "LINC00467" "BEX3" "RAB37" "H2BC4"
## [9] "H2AC20" "MTCP1" "GOLGA8B" "AC023590.1"
## [13] "ZNF451-AS1" "WEE2-AS1" "PCDH9-AS2" "RP11-142A5.1"
## [17] "KCNMA1-AS1" "RP11-544A12.4" "RP5-1101C3.1" "RP11-115J16.1"
## [21] "RP11-120A1.1" "RP11-463D19.1" "RP11-511B23.2" "RP1-71H24.1"
## [25] "TCF4-AS1" "RP11-126O1.4" "TSIX" "H2AC19"
## [29] "RP11-386I14.4" "H2BC8" "H2AC8" "H2BC7"
## [33] "TRG-AS1" "RP11-275G7.2" "GS1-98E2.1" "RP11-21M24.6"
## [37] "RP11-314E10.1" "RP11-399K19.1" "NIBAN2"
## [1] "found 15 genes."
## [1] 29
## [1] "CD74" "CST3" "OGN" "SLC2A9"
## [5] "FLVCR2" "XAF1" "ITM2C" "SMAD6"
## [9] "PTH2R" "LY96" "COPG2" "C1QC"
## [13] "S100Z" "C1QB" "RTTN" "PROS1"
## [17] "CHSY3" "FIRRE" "LINC00894" "RP11-574F11.4"
## [21] "TRHDE" "RASSF2" "MAN1A1" "FRMD4B"
## [25] "COL5A1" "CHSY1" "TLR2" "NGLY1"
## [29] "CDCP1" "NPTX1" "LRFN4" "TLR5"
## [33] "PELI1" "GK" "ZNF277" "UBXN2B"
## [37] "ZNF407"
## [1] "found 34 genes."
## [1] 30
## [1] "PRDM11" "CFAP74" "RTN4RL1" "KCNT1"
## [5] "BICRAL" "SEMA6D" "ZNF365" "RBMS3"
## [9] "NPAS3" "SPOCK1" "CFAP251" "CAMK2N1"
## [13] "GABRB1" "LRFN5" "PDZRN4" "HTR1E"
## [17] "GPC5" "KCTD16" "GLDN" "PTPRT"
## [21] "NPIPB15" "ZNF846" "TAFA2" "FAM155A"
## [25] "MEG3" "MIAT" "RP5-864K19.4" "ARL17B"
## [29] "SHISA9" "RP11-111A21.1" "RP11-707P17.1" "RP11-368L12.1"
## [33] "RP11-396B14.2" "IQCJ-SCHIP1" "RP11-114N19.3" "RP11-358F13.1"
## [37] "RP11-335E8.3" "RP11-452F19.4"
## [1] "found 26 genes."
## [1] 31
## [1] "TTC7A" "SP140" "ARHGEF18" "TMEM241"
## [5] "ARL5C" "BEND6" "ENPP3" "C4orf19"
## [9] "MAMDC2" "LIPC" "ZMAT3" "MARCHF3"
## [13] "SCFD2" "CDIN1" "KBTBD12" "LINC01356"
## [17] "LINC01357" "LINC00539" "AC105760.2" "LINC01141"
## [21] "LINC01684" "KCNMB2-AS1" "ARHGAP8" "XACT"
## [25] "PTCHD4" "LINC00968" "MEF2C-AS1" "RP11-541P9.3"
## [29] "ZNF10" "RP11-630C16.2" "RP11-493L12.4" "LINC00907"
## [33] "ATP6V0D1-DT" "RP11-437L7.2" "RP11-111G13.1" "RP4-545L17.11"
## [37] "RP11-168F24.3" "STAB1" "AC025171.1" "CTB-41I6.2"
## [1] "found 19 genes."
## [1] 32
## [1] "ZNF532" "OPHN1" "PIGL" "MS4A4A" "TENT5A"
## [6] "LDAH" "MTERF1" "PUDP" "SLC49A4" "FBN2"
## [11] "WDPCP" "PID1" "CLIC2" "RAB28" "NMNAT3"
## [16] "TMEM144" "CCDC171" "ACYP2" "FGGY" "WDR25"
## [21] "PCED1B" "RNLS" "B3GLCT" "LINC01285" "PRDX6-AS1"
## [26] "ZNF433-AS1" "FTCDNL1" "SLC16A1-AS1" "TEX41" "ZRANB2-AS2"
## [31] "RFX3-AS1" "LINC01376" "LINC01184" "RP11-319G6.1" "CTB-161M19.4"
## [36] "C8orf37-AS1" "PRANCR" "LINC01146" "MMP28" "RP1-111C20.3"
## [1] "found 25 genes."
## [1] 33
## [1] "OSBPL6" "PDE4D" "RALGPS2" "RFC3" "PIGK" "MAGI1"
## [7] "PTPN14" "SETBP1" "TIAM1" "PLEKHA7" "ATAD5" "DNAH14"
## [13] "WWC3" "PLEKHA5" "PDE4A" "CUX2" "RLF" "ESYT2"
## [19] "DENND1A" "MAPK8IP1" "STARD13" "AGAP3" "DENND4C" "WDR45B"
## [25] "RIT2" "SRSF12" "AGAP1" "FAM110B" "ROBO1" "TANC2"
## [31] "FAM20C" "CADM1" "PDE4B" "SIPA1L1" "RGL3"
## [1] "found 35 genes."
## [1] 34
## [1] "TXNDC16" "PCSK1N"
## [3] "LRRC6" "CALY"
## [5] "LPAR6" "UNC80"
## [7] "GPR85" "SKA2"
## [9] "ERC2" "COL5A2"
## [11] "AC011288.2" "ALG1L9P_ENSG00000248671"
## [13] "CTD-2537O9.1" "CEROX1"
## [15] "RP11-305E17.8" "COPG2IT1"
## [17] "ADAM22" "RAPGEF4"
## [19] "ANKRD12" "RAPGEF1"
## [21] "PPFIA2" "CDH18"
## [23] "FMN2" "FMNL2"
## [25] "CLASP2" "OXR1"
## [27] "LRP1B" "DLGAP1"
## [29] "RIMS2" "CSMD1"
## [31] "OPCML" "RALYL"
## [33] "KCNIP4" "MYT1L"
## [35] "MAGI2" "COL27A1"
## [37] "NEAT1" "SAP30-DT"
## [1] "found 29 genes."
## [1] 35
## [1] "PRKCQ" "MTHFD2L" "PRKCH" "ARAP2" "ZFAT"
## [6] "MYO9A" "SESN1" "ZNF586" "DOCK3" "DCUN1D4"
## [11] "WNT2B" "RGL1" "CAMKMT" "AMN1" "RASGRP3"
## [16] "AGPAT5" "ADK" "CDC42SE2" "EPB41" "STARD9"
## [21] "NEK10" "RNF150" "MALT1" "SLC35E3" "ZHX2"
## [26] "AIDA" "ARL4C" "CARD11" "LINC00862" "DENND1B"
## [31] "C17orf67" "SOGA3" "KLF3-AS1" "AC092835.2" "RP1-179N16.6"
## [36] "SELENOP" "HCG17" "C2orf27A"
## [1] "found 32 genes."
## [1] 36
## [1] "MBNL3" "P3H2" "APBA1" "GCNT2"
## [5] "PEX7" "AKAP7" "SLC10A7" "RAB38"
## [9] "DTD1" "METTL25" "LANCL2" "DPH6"
## [13] "ARHGAP20" "ARMH4" "LRIG1" "CD226"
## [17] "MAP3K7CL" "TNFRSF13C" "PUS10" "MBOAT1"
## [21] "CAPS2" "LEKR1" "LIN52" "LINC00630"
## [25] "RP11-162D16.2" "MIR646HG" "C12orf75" "RP11-381K20.2"
## [29] "LINC02762" "GMDS-DT" "RP11-679C8.2" "LINC02328"
## [33] "RP11-323I15.5" "KLHL24" "SLC35E1" "IL15"
## [37] "TMEM65"
## [1] "found 28 genes."
## [1] 37
## [1] "SLC26A4" "PLGRKT" "MAP3K8" "PLEK" "CENPK"
## [6] "MIS18BP1" "SAT1" "ZSCAN5A" "PCBD2" "EPSTI1"
## [11] "AHI1" "SLC22A23" "BCAS3" "TRPC1" "SLC25A25"
## [16] "C11orf49" "PSTPIP2" "CACNA1D" "BTG2" "ANO10"
## [21] "CDYL2" "PBX3" "XKR6" "MX2" "APOO"
## [26] "KIAA0825" "ZFP36L1" "SRGAP3" "CDKN2B-AS1" "JARID2"
## [31] "MSR1" "CTNNA2" "UBE2R2" "MGAT1" "RNF144B"
## [36] "TNFAIP8" "RASSF3" "ACOT11"
## [1] "found 36 genes."
## [1] 38
## [1] "SNCAIP" "RPH3A" "LRRC74A" "MEIS1" "RORA" "RAB27A" "SMARCD3"
## [8] "CELF4" "TBL1X" "NPDC1" "EPHA4" "AKT3" "EMILIN2" "DRAM1"
## [15] "KCNH1" "PAM" "CLVS2" "LRRC4C" "CLEC1A" "CRIM1" "PDE3B"
## [22] "KALRN" "ZFPM2" "PPM1E" "ALOX15B" "ZDHHC20" "UNC5C" "TSHZ2"
## [29] "EFNA5" "NELL2" "OSBP2" "PBX1" "KAZN" "MIB2" "MICAL3"
## [36] "GRIN2B"
## [1] "found 36 genes."
## [1] 39
## [1] "PKD2L2" "ANGPTL1" "CYREN" "ATP5F1E"
## [5] "OMD" "ACKR4" "IER3" "AGBL3"
## [9] "C11orf65" "CYTL1" "DNAJC24" "RP11-321C24.1"
## [13] "RP4-568F9.6" "ARHGAP15-AS1" "RAP2C-AS1" "LANCL1-AS1"
## [17] "ITGA9-AS1" "FBXO30-DT" "RP11-123B3.2" "RP1-117O3.2"
## [21] "KDM4A-AS1" "RP11-775D22.3" "RP11-796E2.4" "RP11-544A12.8"
## [25] "ANK2-AS1" "FAM198B-AS1" "AC006160.5" "CTD-3239E11.2"
## [29] "RP11-1H15.2" "RP11-571M6.7" "RP11-638I2.8" "RP11-66H6.3"
## [33] "PRKCA-AS1" "RP11-737O24.2" "RP11-622I12.1" "RP11-458A7.1"
## [37] "RP1-80B9.4" "RP11-1H15.4" "RP1-18C9.3" "RP11-6G22.1"
## [41] "CTD-2021K4.2"
## [1] "found 11 genes."
## [1] 40
## [1] "ARSJ" "LINC00639" "RP11-617F9.2" "MAMLD1"
## [5] "RASGRP2" "COL5A3" "LILRB5" "HS3ST2"
## [9] "OLFM1" "PATJ" "BTBD11" "ME3"
## [13] "FBXO32" "PALM2AKAP2" "NRG2" "JAML"
## [17] "PLPP3" "SNED1" "PRICKLE2" "ARHGEF3"
## [21] "STXBP6" "TBC1D10C" "ADGRB1" "H1-10"
## [25] "SLIT1" "LINC00910" "CR1L" "LINC00970"
## [29] "XKR9" "LINC01320" "SATB1-AS1" "LIMD1-AS1"
## [33] "RP11-47I22.3" "CYP1B1-AS1" "TRHDE-AS1" "LINC01322"
## [37] "USP2-AS1" "CPEB2-DT" "RP5-1015P16.1" "RENO1"
## [1] "found 24 genes."
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 4168494 222.7 10243768 547.1 NA 10243768 547.1
## Vcells 8941231 68.3 29538339 225.4 65536 29538339 225.4
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] stringr_1.5.0 limma_3.54.2 tidyr_1.3.0 ggpubr_0.6.0
## [5] ggplot2_3.4.2 data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] Rcpp_1.0.10 png_0.1-8 Biostrings_2.66.0
## [4] digest_0.6.31 utf8_1.2.3 R6_2.5.1
## [7] GenomeInfoDb_1.34.9 backports_1.4.1 stats4_4.2.3
## [10] RSQLite_2.3.1 evaluate_0.20 httr_1.4.6
## [13] pillar_1.9.0 zlibbioc_1.44.0 rlang_1.1.0
## [16] rstudioapi_0.14 car_3.1-2 jquerylib_0.1.4
## [19] blob_1.2.4 R.oo_1.25.0 R.utils_2.12.2
## [22] S4Vectors_0.36.2 rmarkdown_2.21 labeling_0.4.2
## [25] RCurl_1.98-1.12 bit_4.0.5 munsell_0.5.0
## [28] broom_1.0.4 compiler_4.2.3 xfun_0.39
## [31] pkgconfig_2.0.3 BiocGenerics_0.44.0 htmltools_0.5.5
## [34] tidyselect_1.2.0 KEGGREST_1.38.0 GenomeInfoDbData_1.2.9
## [37] tibble_3.2.1 IRanges_2.32.0 fansi_1.0.4
## [40] crayon_1.5.2 dplyr_1.1.2 withr_2.5.0
## [43] R.methodsS3_1.8.2 bitops_1.0-7 grid_4.2.3
## [46] jsonlite_1.8.4 gtable_0.3.3 lifecycle_1.0.3
## [49] DBI_1.1.3 magrittr_2.0.3 scales_1.2.1
## [52] cli_3.6.1 stringi_1.7.12 cachem_1.0.7
## [55] carData_3.0-5 farver_2.1.1 XVector_0.38.0
## [58] ggsignif_0.6.4 bslib_0.4.2 generics_0.1.3
## [61] vctrs_0.6.2 RColorBrewer_1.1-3 org.Hs.eg.db_3.16.0
## [64] tools_4.2.3 bit64_4.0.5 Biobase_2.58.0
## [67] glue_1.6.2 purrr_1.0.1 abind_1.4-5
## [70] fastmap_1.1.1 yaml_2.3.7 AnnotationDbi_1.60.2
## [73] colorspace_2.1-0 rstatix_0.7.2 memoise_2.0.1
## [76] knitr_1.44 sass_0.4.5